Antiviral Drug Discovery Research Articles

Anti-Ebola: an initiative to predict Ebola virus inhibitors through machine learning.

Ebola virus is a deadly pathogen responsible for a frequent series of outbreaks since 1976. Despite various efforts from researchers worldwide, its mortality and fatality are quite high. For antiviral drug discovery, the computational efforts are considered highly useful. Therefore, we have developed an 'anti-Ebola' web server, through quantitative structure–activity relationship information of available molecules with experimental anti-Ebola activities. Three hundred and five unique anti-Ebola compounds with their respective IC50 values were extracted from the ‘DrugRepV’ database. Later, the compounds were used to extract the molecular descriptors, which were subjected to regression-based model development. The robust machine learning techniques, namely support vector machine, random forest and artificial neural network, were employed using tenfold cross-validation. After a randomization approach, the best predictive model showed Pearson's correlation coefficient ranges from 0.83 to 0.98 on training/testing (T274) dataset. The robustness of the developed models was cross-evaluated using William’s plot. The highly robust computational models are integrated into the web server. The ‘anti-Ebola’ web server is freely available at https://bioinfo.imtech.res.in/manojk/antiebola. We anticipate this will serve the scientific community for developing effective inhibitors against the Ebola virus.Graphic abstract Supplementary InformationThe online version contains supplementary material available at 10.1007/s11030-021-10291-7.

A phenomics approach for antiviral drug discovery

BackgroundThe emergence and continued global spread of the current COVID-19 pandemic has highlighted the need for methods to identify novel or repurposed therapeutic drugs in a fast and effective way. Despite the availability of methods for the discovery of antiviral drugs, the majority tend to focus on the effects of such drugs on a given virus, its constituent proteins, or enzymatic activity, often neglecting the consequences on host cells. This may lead to partial assessment of the efficacy of the tested anti-viral compounds, as potential toxicity impacting the overall physiology of host cells may mask the effects of both viral infection and drug candidates. Here we present a method able to assess the general health of host cells based on morphological profiling, for untargeted phenotypic drug screening against viral infections.ResultsWe combine Cell Painting with antibody-based detection of viral infection in a single assay. We designed an image analysis pipeline for segmentation and classification of virus-infected and non-infected cells, followed by extraction of morphological properties. We show that this methodology can successfully capture virus-induced phenotypic signatures of MRC-5 human lung fibroblasts infected with human coronavirus 229E (CoV-229E). Moreover, we demonstrate that our method can be used in phenotypic drug screening using a panel of nine host- and virus-targeting antivirals. Treatment with effective antiviral compounds reversed the morphological profile of the host cells towards a non-infected state.ConclusionsThe phenomics approach presented here, which makes use of a modified Cell Painting protocol by incorporating an anti-virus antibody stain, can be used for the unbiased morphological profiling of virus infection on host cells. The method can identify antiviral reference compounds, as well as novel antivirals, demonstrating its suitability to be implemented as a strategy for antiviral drug repurposing and drug discovery.

A Novel Small Molecule Inhibits Hepatitis C Virus Propagation in Cell Culture.

ABSTRACTHepatitis C virus (HCV) can cause acute and chronic infection that is associated with considerable liver-related morbidity and mortality. In recent years, there has been a shift in the treatment paradigm with the discovery and approval of agents that target specific proteins vital for viral replication. We employed a cell culture-adapted strain of HCV and human hepatoma-derived cells lines to test the effects of our novel small-molecule compound (AO13) on HCV. Virus inhibition was tested by analyzing RNA replication, protein expression, and virus production in virus-infected cells treated with AO13. Treatment with AO13 inhibited virus spread in cell culture and showed a 100-fold reduction in the levels of infectious virus production. AO13 significantly reduced the level of viral RNA contained within cell culture fluids and reduced the cellular levels of HCV core protein, suggesting that the compound might act on a late step in the viral life cycle. Finally, we observed that AO13 did not affect the release of infectious virus from infected cells. Docking studies and molecular dynamics analyses suggested that AO13 might target the NS5B RNA polymerase, however, real-time RT-PCR analyses of cellular levels of HCV RNA showed only an ∼2-fold reduction in viral RNA levels in the presence of AO13. Taken together, this study revealed that AO13 showed consistent, but low-level antiviral effect against HCV, although the mechanism of action remains unclear.IMPORTANCE The discovery of curative antiviral drugs for a chronic disease such as HCV infection has encouraged drug discovery in the context of other viruses for which no curative drugs currently exist. Since we currently face a novel virus that has caused a pandemic, the need for new antiviral agents is more apparent than ever. We describe here a novel compound that shows a modest antiviral effect against HCV that could serve as a lead compound for future drug development against other important viruses such as SARS-CoV-2.

English

In Pakistan, the poultry industry is one of the rapidly growing industries. Due to lack of biosecurity measures, this is affected by some important infectious agents such as Avian Influenza virus (H9N2) and Newcastle disease virus (NDV) results in a huge economic loss. So, to control these losses discovery of new anti-viral drugs required to bring into line to fight against these infections. It is a general perception that the active components of medicinal plants have effective results against various infections like the influenza virus. The current therapeutic facilities need to be improved by investigating new antiviral drugs from natural resources to fight against viral infections. The present study was conducted on ethanolic extracts of seven different flowers to examine their antiviral activity against NDV and H9N2 in ovo using chicken embryonated egg inoculation. The spot agglutination and hemagglutination tests showed inhibitory effects of Rosa damascena Miller, Achillea millefolium, Woodfordia fruticosa Kurtz and Bombax ceiba L. against NDV as no agglutination observed. While the extracts of Taxacum officianale Weber, Hyssopus officianalis L. and Chrysanthemum cinerafolium (Trevis.) Vis. showed positive results for both spot agglutination and hemagglutination assay against NDV. However, both spot agglutination and hemagglutination assay showed inhibitory effect of all the flowers extracts against H9N2. The bioactive components such as alkaloids, ethers, terpenoids, etc. of each flower were analyzed through Gas chromatography mass spectrometry (GC-MS). The current results revealed that ethanolic extracts of these flowers possess strong antiviral activity because of their active ingredients. These ingredients should be isolated, commercialized and used for therapeutic purpose. © 2021 Friends Science Publishers

Development of Broad-Spectrum Antiviral Agents-Inspiration from Immunomodulatory Natural Products.

Developing broad-spectrum antiviral drugs remains an important issue as viral infections continue to threaten public health. Host-directed therapy is a method that focuses on potential targets in host cells or the body, instead of viral proteins. Its antiviral effects are achieved by disturbing the life cycles of pathogens or modulating immunity. In this review, we focus on the development of broad-spectrum antiviral drugs that enhance the immune response. Some natural products present antiviral effects mediated by enhancing immunity, and their structures and mechanisms are summarized here. Natural products with immunomodulatory effects are also discussed, although their antiviral effects remain unknown. Given the power of immunity and the feasibility of host-directed therapy, we argue that both of these categories of natural products provide clues that may be beneficial for the discovery of broad-spectrum antiviral drugs.

Rapid structure-based identification of potential SARS-CoV-2 main protease inhibitors.

The COVID-19 outbreak has thrown the world into an unprecedented crisis. It has posed a challenge to scientists around the globe who are working tirelessly to combat this pandemic. We herein report a set of molecules that may serve as possible inhibitors of the SARS-CoV-2 main protease. To identify these molecules, we followed a combinatorial structure-based strategy, which includes high-throughput virtual screening, molecular docking and WaterMap calculations. The study was carried out using Protein Data Bank structures 5R82 and 6Y2G. DrugBank, Enamine, Natural product and Specs databases, along with a few known antiviral drugs, were used for the screening. WaterMap analysis aided in the recognition of high-potential molecules that can efficiently displace binding-site waters. This study may help the discovery and development of antiviral drugs against SARS-CoV-2.

Mapping the intellectual structure of the coronavirus field (2000-2020): a co-word analysis.

Over the two last decades, coronaviruses have affected human life in different ways, especially in terms of health and economy. Due to the profound effects of novel coronaviruses, growing tides of research are emerging in various research fields. This paper employs a co-word analysis approach to map the intellectual structure of the coronavirus literature for a better understanding of how coronavirus research and the disease itself have developed during the target timeframe. A strategic diagram has been drawn to depict the coronavirus domain’s structure and development. A detailed picture of coronavirus literature has been extracted from a huge number of papers to provide a quick overview of the coronavirus literature. The main themes of past coronavirus-related publications are (a) “Antibody-Virus Interactions,” (b) “Emerging Infectious Diseases,” (c) “Protein Structure-based Drug Design and Antiviral Drug Discovery,” (d) “Coronavirus Detection Methods,” (e) “Viral Pathogenesis and Immunity,” and (f) “Animal Coronaviruses.” The emerging infectious diseases are mostly related to fatal diseases (such as Middle East respiratory syndrome, severe acute respiratory syndrome, and COVID-19) and animal coronaviruses (including porcine, turkey, feline, canine, equine, and bovine coronaviruses and infectious bronchitis virus), which are capable of placing animal-dependent industries such as the swine and poultry industries under strong economic pressure. Although considerable research into coronavirus has been done, this unique field has not yet matured sufficiently. Therefore, “Antibody-virus Interactions,” “Emerging Infectious Diseases,” and “Coronavirus Detection Methods” hold interesting, promising research gaps to be both explored and filled in the future.

Unlocking G-Quadruplexes as Antiviral Targets.

Guanine-rich DNA and RNA sequences can fold into noncanonical nucleic acid structures called G-quadruplexes (G4s). Since the discovery that these structures may act as scaffolds for the binding of specific ligands, G4s aroused the attention of a growing number of scientists. The versatile roles of G4 structures in viral replication, transcription, and translation suggest direct applications in therapy or diagnostics. G4-interacting molecules (proteins or small molecules) may also affect the balance between latent and lytic phases, and increasing evidence reveals that G4s are implicated in generally suppressing viral processes, such as replication, transcription, translation, or reverse transcription. In this review, we focus on the discovery of G4s in viruses and the role of G4 ligands in the antiviral drug discovery process. After assessing the role of viral G4s, we argue that host G4s participate in immune modulation, viral tumorigenesis, cellular pathways involved in virus maturation, and DNA integration of viral genomes, which can be potentially employed for antiviral therapeutics. Furthermore, we scrutinize the impediments and shortcomings in the process of studying G4 ligands and drug discovery. Finally, some unanswered questions regarding viral G4s are highlighted for prospective future projects. SIGNIFICANCE STATEMENT: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition during the last few decades. First identified as relevant targets in oncology, their importance in virology is now increasingly clear. A number of G-quadruplex ligands are known: viral transcription and replication are the main targets of these ligands. Both viral and cellular G4s may be targeted; this review embraces the different aspects of G-quadruplexes in both host and viral contexts.

A Convenient and Biosafe Replicon with Accessory Genes of SARS-CoV-2 and Its Potential Application in Antiviral Drug Discovery.

SARS-CoV-2 causes the pandemic of COVID-19 and no effective drugs for this disease are available thus far. Due to the high infectivity and pathogenicity of this virus, all studies on the live virus are strictly confined in the biosafety level 3 (BSL3) laboratory but this would hinder the basic research and antiviral drug development of SARS-CoV-2 because the BSL3 facility is not commonly available and the work in the containment is costly and laborious. In this study, we constructed a reverse genetics system of SARS-CoV-2 by assembling the viral cDNA in a bacterial artificial chromosome (BAC) vector with deletion of the spike (S) gene. Transfection of the cDNA into cells results in the production of an RNA replicon that keeps the capability of genome or subgenome replication but is deficient in virion assembly and infection due to the absence of S protein. Therefore, such a replicon system is not infectious and can be used in ordinary biological laboratories. We confirmed the efficient replication of the replicon by demonstrating the expression of the subgenomic RNAs which have similar profiles to the wild-type virus. By mutational analysis of nsp12 and nsp14, we showed that the RNA polymerase, exonuclease, and cap N7 methyltransferase play essential roles in genome replication and sgRNA production. We also created a SARS-CoV-2 replicon carrying a luciferase reporter gene and this system was validated by the inhibition assays with known anti-SARS-CoV-2 inhibitors. Thus, such a one-plasmid system is biosafe and convenient to use, which will benefit both fundamental research and development of antiviral drugs.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12250-021-00385-9.

Compelling Evidence for the Activity of Antiviral Peptides against SARS-CoV-2.

Multiple outbreaks of epidemic and pandemic viral diseases have occurred in the last 20 years, including those caused by Ebola virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence or re-emergence of such diseases has revealed the deficiency in our pipeline for the discovery and development of antiviral drugs. One promising solution is the extensive library of antimicrobial peptides (AMPs) produced by all eukaryotic organisms. AMPs are widely known for their activity against bacteria, but many possess additional antifungal, antiparasitic, insecticidal, anticancer, or antiviral activities. AMPs could therefore be suitable as leads for the development of new peptide-based antiviral drugs. Sixty therapeutic peptides had been approved by the end of 2018, with at least another 150 in preclinical or clinical development. Peptides undergoing clinical trials include analogs, mimetics, and natural AMPs. The advantages of AMPs include novel mechanisms of action that hinder the evolution of resistance, low molecular weight, low toxicity toward human cells but high specificity and efficacy, the latter enhanced by the optimization of AMP sequences. In this opinion article, we summarize the evidence supporting the efficacy of antiviral AMPs and discuss their potential to treat emerging viral diseases including COVID-19.

Dengue structural proteins as antiviral drug targets: Current status in the drug discovery & development.

Dengue virus belongs to the class of RNA viruses and subclass of enveloped single-stranded positive-sense RNA virus. It causes dengue fever (DF), dengue hemorrhagic fever (DHF), or dengue shock syndrome (DSS), where DHF and DSS are life-threatening. Even though dengue is an age-old disease, it is still a mystery and continues to be a global threat. Numerous attempts have been carried out in the past few decades to eradicate the virus through vaccine and antiviral drugs, but still battle continues. In this review, the possible drug targets for discovery and development of potential antiviral drugs against structural proteins of dengue virus, the current development status of the antiviral drugs against dengue around the world, and challenges that need to be addressed to overcome the shortcomings in the process of drug discovery have been discussed.

Neuropilin 1: A Novel Entry Factor for SARS-CoV-2 Infection and a Potential Therapeutic Target.

The novel coronavirus disease 2019 (COVID-19) pandemic is severely challenging the healthcare systems and economies of the world, which urgently demand vaccine and therapy development to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, advancing our understanding of the comprehensive entry mechanisms of SARS-CoV-2, especially the host factors that facilitate viral infection, is crucial for the discovery of effective vaccines and antiviral drugs. SARS-CoV-2 has previously been documented to reach cells by binding with ACE2 and CD147 receptors in host cells that interact with the spike (S) protein of SARS-CoV-2. A novel entry factor, called neuropilin 1(NRP1), has recently been discovered as a co-receptor facilitating the entry of SARS-CoV-2. NRP1 is a single-pass transmembrane glycoprotein widely distributed throughout the tissues of the body and acts as a multifunctional co-receptor to bind with different ligand proteins and play diverse physiological roles as well as pathological and therapeutic roles in different clinical conditions/diseases, including COVID-19. The current review, therefore, briefly provides the overview of SARS-CoV-2 entry mechanisms, the structure of NRP1, and their roles in health and various diseases, as well as extensively discusses the current understanding of the potential implication of NRP1 in SARS-CoV-2 entry and COVID-19 treatment.

Live-Cell Analysis of Human Cytomegalovirus DNA Polymerase Holoenzyme Assembly by Resonance Energy Transfer Methods.

Human cytomegalovirus (HCMV) genome replication is a complex and still not completely understood process mediated by the highly coordinated interaction of host and viral products. Among the latter, six different proteins form the viral replication complex: a single-stranded DNA binding protein, a trimeric primase/helicase complex and a two subunit DNA polymerase holoenzyme, which in turn contains a catalytic subunit, pUL54, and a dimeric processivity factor ppUL44. Being absolutely required for viral replication and representing potential therapeutic targets, both the ppUL44–pUL54 interaction and ppUL44 homodimerization have been largely characterized from structural, functional and biochemical points of view. We applied fluorescence and bioluminescence resonance energy transfer (FRET and BRET) assays to investigate such processes in living cells. Both interactions occur with similar affinities and can take place both in the nucleus and in the cytoplasm. Importantly, single amino acid substitutions in different ppUL44 domains selectively affect its dimerization or ability to interact with pUL54. Intriguingly, substitutions preventing DNA binding of ppUL44 influence the BRETmax of protein–protein interactions, implying that binding to dsDNA induces conformational changes both in the ppUL44 homodimer and in the DNA polymerase holoenzyme. We also compared transiently and stably ppUL44-expressing cells in BRET inhibition assays. Transient expression of the BRET donor allowed inhibition of both ppUL44 dimerization and formation of the DNA polymerase holoenzyme, upon overexpression of FLAG-tagged ppUL44 as a competitor. Our approach could be useful both to monitor the dynamics of assembly of the HCMV DNA polymerase holoenzyme and for antiviral drug discovery.

Discovery of an imidazonaphthyridine and a riminophenazine as potent anti-Zika virus agents through a replicon-based high-throughput screening

The 2015/16 Zika virus (ZIKV) epidemic led to almost 1 million confirmed cases in 84 countries and was associated to the development of congenital microcephaly and Guillain-Barré syndrome. More recently, a ZIKV African lineage was identified in Brazil raising concerns about a future outbreak. The long-term consequences of viral infection emphasizes the need for the development of effective anti-ZIKV drugs. In this study, we developed and characterized a ZIKV replicon cell line for the screening of viral replication inhibitors. The replicon system was developed by engineering the IRES-Neo cassette into the 3’ UTR terminus of the ZIKV Rluc DNA construct. After in vitro transcription, replicon RNA was used to transfect BHK-21 cells, that were selected with G418, thus generating the BHK-21-RepZIKV_IRES-Neo cell line. Through this replicon-based cell system, we identified two molecules with potent anti-ZIKV activities, an imidazonaphthyridine and a riminophenazine, both from the MMV/DNDi Pandemic Response Box library of 400 drug-like compounds. The imidazonaphthyridine, known as RO8191, showed remarkable selectivity against ZIKV, while the riminophenazine, the antibiotic Clofazimine, could act as a non-nucleoside analog inhibitor of viral RNA-dependent RNA polymerase (RdRp), as evidenced both in vitro and in silico. The data showed herein supports the use of replicon-based assays in high-throughput screening format as a biosafe and reliable tool for antiviral drug discovery.

Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation.

BackgroundThe COVID-19 pandemic, caused by the SARS-CoV-2 virus, has ravaged lives across the globe since December 2019, and new cases are still on the rise. Peoples’ ongoing sufferings trigger scientists to develop safe and effective remedies to treat this deadly viral disease. While repurposing the existing FDA-approved drugs remains in the front line, exploring drug candidates from synthetic and natural compounds is also a viable alternative. This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime molecular target to treat coronavirus diseases.MethodsWe performed 100 ns GROMACS molecular dynamics simulations of three high-resolution X-ray crystallographic structures of 3CL-PRO. We extracted frames at 10 ns intervals to mimic conformational diversities of the target protein in biological environments. We then used AutoDock Vina molecular docking to virtual screen the Sigma–Aldrich MyriaScreen Diversity Library II, a rich collection of 10,000 druglike small molecules with diverse chemotypes. Subsequently, we adopted in silico computation of physicochemical properties, pharmacokinetic parameters, and toxicity profiles. Finally, we analyzed hydrogen bonding and other protein-ligand interactions for the short-listed compounds.ResultsOver the 100 ns molecular dynamics simulations of 3CL-PRO’s crystal structures, 6LZE, 6M0K, and 6YB7, showed overall integrity with mean Cα root-mean-square deviation (RMSD) of 1.96 (±0.35) Å, 1.98 (±0.21) Å, and 1.94 (±0.25) Å, respectively. Average root-mean-square fluctuation (RMSF) values were 1.21 ± 0.79 (6LZE), 1.12 ± 0.72 (6M0K), and 1.11 ± 0.60 (6YB7). After two phases of AutoDock Vina virtual screening of the MyriaScreen Diversity Library II, we prepared a list of the top 20 ligands. We selected four promising leads considering predicted oral bioavailability, druglikeness, and toxicity profiles. These compounds also demonstrated favorable protein-ligand interactions. We then employed 50-ns molecular dynamics simulations for the four selected molecules and the reference ligand 11a in the crystallographic structure 6LZE. Analysis of RMSF, RMSD, and hydrogen bonding along the simulation trajectories indicated that S51765 would form a more stable protein-ligand complexe with 3CL-PRO compared to other molecules. Insights into short-range Coulombic and Lennard-Jones potentials also revealed favorable binding of S51765 with 3CL-PRO.ConclusionWe identified a potential lead for antiviral drug discovery against the SARS-CoV-2 main protease. Our results will aid global efforts to find safe and effective remedies for COVID-19.

Unveiling ancestral relations, host–pathogen interactions and comparative viral miRNA insights of dengue virus serotypes

Dengue fever is the most widespread mosquito-borne viral disease caused by the four serotypes of Dengue virus that belong to the Genus Flavivirus (family Flaviviridae). The diversity of serotype makes the diseases fatal with the possibility to be infected four times and makes complications in the antiviral drug discovery process. In this study, we analyzed the genomic diversity along with phylogenetical relations of the complete genome of four dengue virus serotypes found in different regions in the world. Viral pathogen and its host (human, mosquito) protein–protein interactions (PPIs) have been performed to reveal the connection between the proteins of host and pathogen. The analysis revealed that DENV3 and DENV1 strains are closely related, whereas the other 2 strains (DENV2 and DENV4) are distinctly related. DENV-2 serotype has been supposed to be more virulent, because more epidemics of dengue hemorrhagic fever have been associated with it than with the other serotypes. PPIs between dengue virus proteins obtained from Bangladesh regions and its host revealed that dengue–human PPIs are more prevail in DENV2 and DENV3 serotypes, whereas dengue–mosquito PPIs are most predominant in DENV1 serotype. Moreover, precursor miRNAs and their respective mature miRNAs are also predicted that may provide more clear insight into dengue virus pathogenesis. The present analysis provides detailed pictures of the origin, evolution, and genetic mutations of the dengue virus serotypes. This study can facilitate one stepping stone in the development and production of preventive, affordable, and safe antiviral medications.

Enantiomeric 4′-truncated 6′-fluoro-3-deazaneplanocin and its 3-bromo derivative: Synthesis and antiviral properties, including Ebola and Marburg

In seeking to increase the library of fluorine containing adenine-derived carbocyclic nucleoside antiviral candidates, d-like and l-like 6′-fluoro-3-deazaneplanocin and its 3-bromo derivative lacking the 4′-hydroxylmethylene substituent (2/3 and 4/5, respectively) are presented. Their synthesis was accomplished from d-ribose by developing a more facile precursor route than suggested by the literature. The 2/4d-like pair displayed significant anti-filo virial properties while the enantiomeric l-like congeners 3/5 were inactive. Target compounds 2/4 also were active towards measles and norovirus. The effect of 2/4 is further evidence of the role fluoro-derived adenine carbocyclic nucleoside can play in antiviral drug discovery. Furthermore, the simplicity of their synthesis lends them to more efficacious analogs and to scale-up optimization. There were no other relevant antiviral properties for 2/3 and 4/5 (except BK polyomavirus for 3/5).

Computational studies by molecular docking of some antiviral drugs with COVID-19 receptors are an approach to medication for COVID-19

Abstract The COVID-19 outbreak is a matter of concern worldwide due to unavailability of promising treatment comprising medication or vaccination till date. The discovery of antiviral drug is of immense importance in the existing spread of novel coronavirus. The goal of the present study was to evolve an opposite antiviral drug against the novel COVID-19 virus. A directly succeeding perspective would be to use the prevailing influential drugs from several antimicrobial and chemotherapeutic agents. The encouraging approach is to identify promising drug molecules and compounds through virtual screening via molecular docking of FDA-approved drugs and some previously synthesized pyridone and coumarin derivatives for probable therapeutic outcome. In this conceptual milieu, an effort has been made to propose a computational in silico relationship among FDA-approved drugs and coronavirus-associated receptors and proteins. The study results were evaluated on the basis of a dock score by using molecular operating environment. Out of 15 compounds screened, the compounds with the best docking scores toward their targets was 3d. Therefore, compound 3d deserves further investigations and clinical trials as a possible therapeutic inhibitor of the COVID-19 caused by the novel SARS-CoV-2.

Development of A MERS-CoV Replicon Cell Line for Antiviral Screening.

Middle East respiratory syndrome coronavirus (MERS-CoV) is the causative agent of a severe respiratory disease with a high mortality of ~ 35%. The lack of approved treatments for MERS-CoV infection underscores the need for a user-friendly system for rapid drug screening. In this study, we constructed a MERS-CoV replicon containing the Renilla luciferase (Rluc) reporter gene and a stable luciferase replicon-carrying cell line. Using this cell line, we showed that MERS-CoV replication was inhibited by combined application of lopinavir and ritonavir, indicating that this cell line can be used to screen inhibitors of MERS-CoV replication. Importantly, the MERS-replicon cell line can be used for high-throughput screening of antiviral drugs without the need for live virus handling, providing an effective and safe tool for the discovery of antiviral drugs against MERS-CoV.Electronic supplementary materialThe online version of this article (10.1007/s12250-020-00341-z) contains supplementary material, which is available to authorized users.

Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches.

Coronavirus disease-19 (COVID-19) pandemic, caused by the novel SARS-CoV-2 virus, continues to be a global threat. The number of cases and deaths will remain escalating due to the lack of effective therapeutic agents. Several studies have established the importance of the viral main protease (Mpro) in the replication of SARS-CoV-2 which makes it an attractive target for antiviral drug development, including pharmaceutical repurposing and other medicinal chemistry approaches. Identification of natural products with considerable inhibitory potential against SARS-CoV-2 could be beneficial as a rapid and potent alternative with drug-likeness by comparison to de novo antiviral drug discovery approaches. Thereof, we carried out the structure-based screening of natural products from Echinacea-angustifolia, commonly used to prevent cold and other microbial respiratory infections, targeting SARS-CoV-2 Mpro. Four natural products namely, Echinacoside, Quercetagetin 7-glucoside, Levan N, Inulin from chicory, and 1,3-Dicaffeoylquinic acid, revealed significant docking energy (>−10 kcal/mol) in the SARS-CoV-2 Mpro catalytic pocket via substantial intermolecular contacts formation against co-crystallized ligand (<−4 kcal/mol). Furthermore, the docked poses of SARS-CoV-2 Mpro with selected natural products showed conformational stability through molecular dynamics. Exploring the end-point net binding energy exhibited substantial contribution of Coulomb and van der Waals interactions to the stability of respective docked conformations. These results advocated the natural products from Echinacea angustifolia for further experimental studies with an elevated probability to discover the potent SARS-CoV-2 Mpro antagonist with higher affinity and drug-likeness.